App configuration

config.ini

All configuration is defined in config.ini. Note that there are no apostrophes (" or ') in this file.

[auth]

auth_file
A file path to where authentication details for DHIS2 and ODK Aggregate are stored - see dish.json for structure of the file. Keep it on a secure place and refer to its file path.

[logging]

logfile
Where the application should log to, e.g. /var/log/smartvadhis2.log
level
Minimum Log level - e.g. INFO logs all info messages, warnings, errors. Must be one of: DEBUG, INFO, WARNINGS

[database]

db_queries_log
Whether to log all local database queries as well. Either true or false.
db_name
Name of the local database file, e.g. smartva-dhis2.db

[odk]

form_id
Verbal Autopsy ODK Form ID, e.g. SmartVA_Bangla_v7
sid_regex
Regular Expression that matches a to Verbal Autopsy Study ID number, e.g. ^VA_[0-9]{17}$. Check regex with online tools, e.g. regex101.com. If you want to allow any SID format (not recommended), you can put sid_regex = .*.

[smartva]

ignore_columns
Which CSV columns in the SmartVA CSV output to ignore for further processing. Must be delimited by commas , and without space, e.g. geography1,geography2,geography4,geography5,cause34
algorithm_version
With which version the CoD was obtained, e.g. Tariff 2.0.
country
Data origin country abbreviation. See below for full list.
hiv
Data is from an HIV region
malaria
Data is from a Malaria region.
hce
Use Health Care Experience (HCE) variables.

For more information about SmartVA options refer to the SmartVA Help: PDF.

[dhis]

program
The Unique Identifier (UID) of the Verbal Autopsy DHIS2 program.
program_stage
The Unique Identifier (UID) of the Verbal Autopsy DHIS2 program stage.
api_version
DHIS2 API Version (e.g. 28)

For further mapping details see also the smartva/core/mapping.py module.

Org Unit set up

In order to determine the location of the Verbal Autopsy, you need to define the following steps:

  1. Find out where the orgUnit is located in your aggregate CSV
  2. ignore certain columns in the smartva.ignore_columns section of config.ini (see above)
  3. In smartvadhis2/core/mapping.py, update the csv_name property in the Orgunit class.

In the example config.ini, the column holding the Organisation Unit UID is geography3.

Country list

See section [smartva] above.

Country list:

  • Unknown [default]
  • Afghanistan (AFG)
  • Albania (ALB)
  • Algeria (DZA)
  • Andorra (AND)
  • Angola (AGO)
  • Antigua and Barbuda (ATG)
  • Argentina (ARG)
  • Armenia (ARM)
  • Australia (AUS)
  • Austria (AUT)
  • Azerbaijan (AZE)
  • Bahrain (BHR)
  • Bangladesh (BGD)
  • Barbados (BRB)
  • Belarus (BLR)
  • Belgium (BEL)
  • Belize (BLZ)
  • Benin (BEN)
  • Bhutan (BTN)
  • Bolivia (BOL)
  • Bosnia and Herzegovina (BIH)
  • Botswana (BWA)
  • Brazil (BRA)
  • Brunei (BRN)
  • Bulgaria (BGR)
  • Burkina Faso (BFA)
  • Burundi (BDI)
  • Cambodia (KHM)
  • Cameroon (CMR)
  • Canada (CAN)
  • Cape Verde (CPV)
  • Central African Republic (CAF)
  • Chad (TCD)
  • Chile (CHL)
  • China (CHN)
  • Colombia (COL)
  • Comoros (COM)
  • Congo (COG)
  • Costa Rica (CRI)
  • Cote d’Ivoire (CIV)
  • Croatia (HRV)
  • Cuba (CUB)
  • Cyprus (CYP)
  • Czech Republic (CZE)
  • Democratic Republic of the Congo (COD)
  • Denmark (DNK)
  • Djibouti (DJI)
  • Dominica (DMA)
  • Dominican Republic (DOM)
  • Ecuador (ECU)
  • Egypt (EGY)
  • El Salvador (SLV)
  • Equatorial Guinea (GNQ)
  • Eritrea (ERI)
  • Estonia (EST)
  • Ethiopia (ETH)
  • Federated States of Micronesia (FSM)
  • Fiji (FJI)
  • Finland (FIN)
  • France (FRA)
  • Gabon (GAB)
  • Georgia (GEO)
  • Germany (DEU)
  • Ghana (GHA)
  • Greece (GRC)
  • Grenada (GRD)
  • Guatemala (GTM)
  • Guinea (GIN)
  • Guinea-Bissau (GNB)
  • Guyana (GUY)
  • Haiti (HTI)
  • Honduras (HND)
  • Hungary (HUN)
  • Iceland (ISL)
  • India (IND)
  • Indonesia (IDN)
  • Iran (IRN)
  • Iraq (IRQ)
  • Ireland (IRL)
  • Israel (ISR)
  • Italy (ITA)
  • Jamaica (JAM)
  • Japan (JPN)
  • Jordan (JOR)
  • Kazakhstan (KAZ)
  • Kenya (KEN)
  • Kiribati (KIR)
  • Kuwait (KWT)
  • Kyrgyzstan (KGZ)
  • Laos (LAO)
  • Latvia (LVA)
  • Lebanon (LBN)
  • Lesotho (LSO)
  • Liberia (LBR)
  • Libya (LBY)
  • Lithuania (LTU)
  • Luxembourg (LUX)
  • Macedonia (MKD)
  • Madagascar (MDG)
  • Malawi (MWI)
  • Malaysia (MYS)
  • Maldives (MDV)
  • Mali (MLI)
  • Malta (MLT)
  • Marshall Islands (MHL)
  • Mauritania (MRT)
  • Mauritius (MUS)
  • Mexico (MEX)
  • Moldova (MDA)
  • Mongolia (MNG)
  • Montenegro (MNE)
  • Morocco (MAR)
  • Mozambique (MOZ)
  • Myanmar (MMR)
  • Namibia (NAM)
  • Nepal (NPL)
  • Netherlands (NLD)
  • New Zealand (NZL)
  • Nicaragua (NIC)
  • Niger (NER)
  • Nigeria (NGA)
  • North Korea (PRK)
  • Norway (NOR)
  • Oman (OMN)
  • Pakistan (PAK)
  • Palestine (PSE)
  • Panama (PAN)
  • Papua New Guinea (PNG)
  • Paraguay (PRY)
  • Peru (PER)
  • Philippines (PHL)
  • Poland (POL)
  • Portugal (PRT)
  • Qatar (QAT)
  • Romania (ROU)
  • Russia (RUS)
  • Rwanda (RWA)
  • Saint Lucia (LCA)
  • Saint Vincent and the Grenadines (VCT)
  • Samoa (WSM)
  • Sao Tome and Principe (STP)
  • Saudi Arabia (SAU)
  • Senegal (SEN)
  • Serbia (SRB)
  • Seychelles (SYC)
  • Sierra Leone (SLE)
  • Singapore (SGP)
  • Slovakia (SVK)
  • Slovenia (SVN)
  • Solomon Islands (SLB)
  • Somalia (SOM)
  • South Africa (ZAF)
  • South Korea (KOR)
  • Spain (ESP)
  • Sri Lanka (LKA)
  • Sudan (SDN)
  • Suriname (SUR)
  • Swaziland (SWZ)
  • Sweden (SWE)
  • Switzerland (CHE)
  • Syria (SYR)
  • Taiwan (TWN)
  • Tajikistan (TJK)
  • Tanzania (TZA)
  • Thailand (THA)
  • The Bahamas (BHS)
  • The Gambia (GMB)
  • Timor-Leste (TLS)
  • Togo (TGO)
  • Tonga (TON)
  • Trinidad and Tobago (TTO)
  • Tunisia (TUN)
  • Turkey (TUR)
  • Turkmenistan (TKM)
  • Uganda (UGA)
  • Ukraine (UKR)
  • United Arab Emirates (ARE)
  • United Kingdom (GBR)
  • United States (USA)
  • Uruguay (URY)
  • Uzbekistan (UZB)
  • Vanuatu (VUT)
  • Venezuela (VEN)
  • Vietnam (VNM)
  • Yemen (YEM)
  • Zambia (ZMB)
  • Zimbabwe (ZWE)